COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation

Background Recent single-center reports have suggested that community-acquired bacteremic co-infection in the context of Coronavirus disease 2019 (COVID-19) may be an important driver of mortality; however, these reports have not been validated with a multicenter, demographically diverse, cohort study with data spanning the pandemic. Methods In this multicenter, retrospective cohort study, inpatient encounters were assessed for COVID-19 with community-acquired bacteremic co-infection using 48-h post-admission blood cultures and grouped by: (1) confirmed co-infection [recovery of bacterial pathogen], (2) suspected co-infection [negative culture with ≥ 2 antimicrobials administered], and (3) no evidence of co-infection [no culture]. The primary outcomes were in-hospital mortality, ICU admission, and mechanical ventilation. COVID-19 bacterial co-infection risk factors and impact on primary outcomes were determined using multivariate logistic regressions and expressed as adjusted odds ratios with 95% confidence intervals (Cohort, OR 95% CI, Wald test p value). Results The studied cohorts included 13,781 COVID-19 inpatient encounters from 2020 to 2022 in the University of Alabama at Birmingham (UAB, n = 4075) and Ochsner Louisiana State University Health—Shreveport (OLHS, n = 9706) cohorts with confirmed (2.5%), suspected (46%), or no community-acquired bacterial co-infection (51.5%) and a comparison cohort consisting of 99,170 inpatient encounters from 2010 to 2019 (UAB pre-COVID-19 pandemic cohort). Significantly increased likelihood of COVID-19 bacterial co-infection was observed in patients with elevated ≥ 15 neutrophil-to-lymphocyte ratio (UAB: 1.95 [1.21–3.07]; OLHS: 3.65 [2.66–5.05], p < 0.001 for both) within 48-h of hospital admission. Bacterial co-infection was found to confer the greatest increased risk for in-hospital mortality (UAB: 3.07 [2.42–5.46]; OLHS: 4.05 [2.29–6.97], p < 0.001 for both), ICU admission (UAB: 4.47 [2.87–7.09], OLHS: 2.65 [2.00–3.48], p < 0.001 for both), and mechanical ventilation (UAB: 3.84 [2.21–6.12]; OLHS: 2.75 [1.87–3.92], p < 0.001 for both) across both cohorts, as compared to other risk factors for severe disease. Observed mortality in COVID-19 bacterial co-infection (24%) dramatically exceeds the mortality rate associated with community-acquired bacteremia in pre-COVID-19 pandemic inpatients (5.9%) and was consistent across alpha, delta, and omicron SARS-CoV-2 variants. Conclusions Elevated neutrophil-to-lymphocyte ratio is a prognostic indicator of COVID-19 bacterial co-infection within 48-h of admission. Community-acquired bacterial co-infection, as defined by blood culture-positive results, confers greater increased risk of in-hospital mortality, ICU admission, and mechanical ventilation than previously described risk factors (advanced age, select comorbidities, male sex) for COVID-19 mortality, and is independent of SARS-CoV-2 variant. Supplementary Information The online version contains supplementary material available at 10.1186/s13054-023-04312-0.

Reported COVID-19 co-infection rates have ranged from 2 to 8% but consistently appear less than the influenza co-infection rates as reported in the 1918 pandemic and the estimated 34% co-infection rate of the 2009 influenza A (H1N1) pandemic [6,7,[18][19][20]. Mortality rates from COVID-19 co-infection have varied widely from twofold compared to non-co-infected COVID-19 patients, to having no effect on mortality among co-infected ICU patients [5,8,17,21]. Several issues confound a reliable determination of co-infection prevalence and associated morbidity, notably inconsistent definitions of co-infection, limited sample size without independent multicenter cohorts, and inclusion of outpatient encounters in co-infection event rate calculations [5,7]. Here, we defined bacterial co-infection as the presence of a pathogenic isolate from a sterile site, blood, as determined by positive blood cultures taken within 48-h of admission. This approach provides an analysis that discriminates true pathogens from incidental or colonizing organisms, enabling a consistent assessment of co-infection across cohorts and their impact on clinical outcomes.
The primary aims of this retrospective study were to define: (1) the prevalence of COVID-19 co-infections, (2) the impact of COVID-19 co-infection and SARS-CoV-2 variant strain on clinical outcomes including ICU admission, need for invasive mechanical ventilation, and in-hospital mortality utilizing two independent cohorts, and (3) early biomarkers associated with bacterial coinfection. We hypothesized that bacterial co-infection contributes to poor clinical outcomes in COVID-19 subjects irrespective of SARS-CoV-2 variant, and that early recognition of co-infection is possible with routinely gathered laboratory and vital sign measurements.

Study design and population
A multicenter, retrospective cohort study was performed using adult (age: 18-90 years) hospital admissions with a length of stay (LOS) 1-120 days, SARS-CoV-2-positive tests (rapid antigen or polymerase chain reaction) within 48-h of hospital admission, and blood culture evidence of bacterial co-infection in the University of Alabama at Birmingham Health System (UAB) cohort and the Ochsner Louisiana State University Health-Shreveport (OLHS) cohort. The UAB cohort consisted of hospitals from Jefferson, Shelby, and St. Clair counties in Alabama, USA. The OLHS cohort consisted of hospitals across the state of Louisiana, USA. Data extraction was limited to 01/2020-03/2022. Rationale for using blood cultures alone was due to their standardized use, interpretation across both cohorts, and to avoid culture sites where contamination and colonization are prominent. To exclude hospital-acquired infections, we restricted cultures to those collected within 48-h of COVID-19 admission (see Additional file 1: eFig. 1).
COVID-19-positive inpatient encounters were grouped by (1) confirmed bacterial co-infections [positive blood culture(s) taken within 48-h of admission, containing bacterial pathogens; fungal organisms were omitted], (2) clinically suspected co-infections [negative blood culture(s) obtained within 48-h of admission and initiation of treatment with ≥ 2 doses of antimicrobial agents], and (3) no co-infection [no blood cultures collected within 48-h of admission]. Criteria for the confirmed and suspected sub-groupings were modeled after [22] suspected infection international consensus definition and are described in Additional file 1: eFig. 1 [22]. Bacterial organisms recovered from blood culture in the UAB and OLHS cohorts are described in Additional file 1: eFigs. 2-3.
To compare the effect of COVID-19 co-infection on inpatient outcomes to a pre-pandemic cohort, a total of 199,239 COVID-19-negative inpatient encounters from 2010 to 2019 in the UAB health system were assessed for evidence of bacterial infection (Additional file 1: eFig. 8). After exclusion, 99,170 inpatient encounters with adult patients (age: 18-90 years) with a LOS between 1 and 120 days were stratified into confirmed communityacquired bacteremic infection (n = 1703), suspected community-acquired bacteremic infection (n = 11,795), and no community-acquired bacteremic infection (n = 85,672). Detailed information on the pre-COVID-19 pandemic UAB cohort accrual, characteristics, and bacterial pathogens recovered can be found in Additional file 1: eFigs. 8-9, eTable 14.

Data extraction and primary study outcomes
Primary outcomes studied were in-hospital mortality, ICU admission (anytime), and need for invasive mechanical ventilation. Mechanical ventilation was confirmed by the first date of concomitant recordings of endotracheal tube insertion distance and ventilator settings. Presentation severity was assessed using the physiologic and laboratory measurements required for calculating Systemic Inflammatory Response Syndrome scores (SIRS; range 0 [best] to 4 [worst]) [23]. SIRS variables are tachycardia (heart rate > 90 beats/min), tachypnea (respiratory rate > 20 breaths/min), fever or hypothermia (temperature > 38 or < 36 Celsius [C°]), and leukocytosis, leukopenia, or bandemia (white blood cell count < 4 or > 12 × 10 3 /uL or bandemia ≥ 10%). Rationale for using the SIRS criteria was threefold: 1) SIRS variables are routinely gathered across both cohorts within 24-h of hospital admission, 2) data missingness for all SIRS variables was exceedingly low (3.8% of all included encounters), enabling unbiased outcome modeling without use of any data imputation methods, and 3) unlike the World Health Organization (WHO) 8-point ordinal scale of COVID-19 severity, none of the SIRS variables are inherent to ICU admission or use of mechanical ventilation, which permits unconfounded modeling of these important clinical outcomes [24]. Pre-admission Charlson comorbidity scores were computed using ICD-9/10 diagnosis codes taken prior to each inpatient encounter [25].

Statistical analysis
Overall cohort statistics were performed using the Wilcoxon rank-sum test, Pearson's Chi-squared test, or Fisher's exact test and are reported in Additional file 1: eTable 1. Temporal laboratory measurement trends stratified by COVID-19 bacterial co-infection status and assessed from the day of admission (day 0) to 3 days post-admission. Pooled encounters from the UAB and OLHS cohorts were used for this analysis to increase cohort size for early biomarker trend assessment. Statistical differences between COVID-19 co-infection status groups were assessed using Bonferroni corrected t-tests for multiple comparisons between COVID-19 with confirmed (reference), suspected, and no co-infection subgroups.
Multivariable logistic regression models were used to assess pre-and post-admission risk factors for COVID-19 bacterial co-infection in the UAB and OLHS cohorts independently, using two groups (confirmed bacterial co-infection vs a single group comprised of the suspected and no co-infection groups; Fig. 3). Additional sensitivity testing for pre-and post-admission risk factor models was performed using only the confirmed and suspected co-infection groups (Additional file 1: eTable 15). Univariate and multivariate logistic regression models were used to assess the impact of COVID-19 co-infection on primary clinical outcomes including in-hospital mortality, ICU admission, and invasive mechanical ventilation use. Models were built from the UAB and OLHS cohorts independently unless specified. No assumptions or imputations for missing data were made for any model variables (see Additional file 1: eFig. 5 for variable missingness). Co-linearity of model variables was assessed using Spearman correlation analysis (Additional file 1: eFig. 6). Pre-admission COVID-19 co-infection risk factor model variables included age, sex, and pulmonary, renal, cardiac, and diabetic comorbidities as defined by the Charlson comorbidity index [25]. Post-admission risk factor models used all four components of the SIRS scores and neutrophil-to-lymphocyte ratio computed from laboratory and vitals measurements taken within 24-h of admission. Sensitivity testing for outcome models was performed using the blood culture(-) suspected coinfection cohort as a reference group (with and without data imputation for missing comorbidity and 24-h postadmission SIRS scores) and is reported in Additional file 1: eTables 16-34, eFig. 10.
The effect of COVID-19 co-infection on clinical outcomes was assessed using univariate and multivariable logistic regression with advanced age (≥ 65 years), male sex, pre-admission cardiac, pulmonary, diabetic, and renal comorbidities, and co-infection status model variables. All modeling experiments reported as adjusted odds ratios with bootstrapped (n = 1000 iterations) 95% confidence intervals (CI) and the Wald test to determine statistical significance of model variables. All statistical analyses were performed using R (version 4.2, R Foundation).

Population characteristics
A total of 88,756 inpatient encounters from hospitals in the UAB (n = 30,901) and OLHS (n = 57,855) cohorts were assessed in this multicenter retrospective cohort study from 03/2020 to 03/2022. After exclusion, 13,781 inpatient encounters with adult patients (age: 18-90 years), a positive COVID-19 test within 48-h of admission, and a length of stay between 1 and 120 days were further stratified into three groups: confirmed bacterial co-infection, suspected bacterial co-infection, and no bacterial co-infection ( Fig. 1). Baseline demographics, outcomes, and therapeutic interventions for patients in the three COVID-19 co-infection groups are

Temporal laboratory trends and biomarkers for COVID-19 bacterial co-infection
To identify biomarkers associated with COVID-19 coinfection, post-admission laboratory result trends were assessed. Overall, complete blood count (CBC) with differential measurements including white blood cell count, absolute neutrophil count, absolute lymphocyte count, and neutrophil-to-lymphocyte ratio (NLR) were substantially different between confirmed COVID-19 co-infection versus suspected and no co-infection groups (Fig. 2).
We assessed the impact of corticosteroid treatment in COVID-19 management by stratifying the cohort by patients that did or did not receive dexamethasone treatment (within 48-h of admission) and found the NLR remained elevated in the confirmed COVID-19 bacterial co-infection group at each time point post-admission, regardless of dexamethasone treatment (Fig. 2). This finding demonstrates that dexamethasone-induced neutrophilia did not materially influence the observation of high NLR in confirmed bacterial co-infection [26]. Other statistically significant findings for COVID-19 co-infection included elevated lactate and creatinine levels in each post-admission time point, elevated C-reactive protein at the first two time points, and elevated procalcitonin on the day of admission (Additional file 1: eFig. 4).

COVID-19 bacterial co-infection risk factors
Pre-admission and 24-h post-admission risk factors associated with COVID-19 bacterial co-infections were assessed using independent multivariable logistic regression models in the UAB and OLHS cohorts. We observed an increased likelihood of COVID  (Fig. 3).

Impact of COVID-19 bacterial co-infection on clinical outcomes
Multiple risk factors have been associated with COVID-19 severity and mortality including advanced age, male sex, and diabetic, cardiac, renal, and pulmonary comorbidities [4].

Discussion
In this multicenter retrospective study of 13,781 COVID-19 inpatient encounters, our results demonstrate an increased risk of ICU admission, mechanical ventilation, and in-hospital mortality conferred by COVID-19 bacterial co-infection that substantially exceeds previously described risk factors for severity and mortality (e.g., advanced age, male sex, select comorbidities) [4]. The external validity of this result is enhanced by use of data spanning the two years of the pandemic (2020-2022) across two independent cohorts, as well as a 10-year pre-COVID-19 pandemic comparator cohort (2010-2019). Our investigation identified laboratory trends associated with COVID-19 bacterial co-infection and provide evidence that ≥ 15 NLR, temperature, white blood cell count, and heart rate components of the SIRS criterion can help healthcare providers discriminate COVID-19 bacterial co-infections within 24-h of admission. These results emphasize the role of bacteria in SARS-CoV-2 mortality and highlight the potential for NLR as a rapid and easily available prognostic biomarker of bacterial coinfection, and relatedly, disease severity. A strength of this study is the use of large, demographically diverse, independent cohorts. The UAB cohort (n = 4075) reflects an academic hospital and level I trauma center servicing five surrounding states. The OLHS cohort (n = 9706) includes encounters from rural, suburban, and academic medical centers across the state of Louisiana. Despite the different clinical settings, both cohorts overall were well matched for patient age, race, sex, and inpatient LOS. Due to sufficiently sized cohorts, all risk factor and outcome modeling performed in this study did not use any form of imputed data. In agreement with previous studies, we found COVID-19 bacterial coinfection to be relatively infrequent in both UAB (2.5%, n = 110) and OLHS cohorts (2.7%, n = 240), with Staphylococcus aureus and Escherichia coli as the most frequent Gram-positive and Gram-negative pathogens recovered  from 48-h post-admission blood cultures, respectively [5].
Prior studies have explored early biomarkers of COVID-19 co-infections including a 2021 multi-cohort study that reported an elevated baseline white blood cell count and stepwise decrease in CRP at two time points (admission and 48-72-h later) were sufficient to exclude COVID-19 bacterial co-infection in 46% of cases [27]. A crucial limitation to this approach is the requirement of 3 laboratory measurements over a 72-h period, in addition to the modest observed exclusion rate. Here, our results confirm both the elevated CRP and white blood cell count findings as indicators of bacterial co-infection in COVID-19. In addition, we found elevated NLR, lactate, creatinine, and procalcitonin at 24-h post-admission, which raises the possibility of a novel co-infection prediction score that could help overcome the clinical lag associated with culture data and sequential (48-72-h later) laboratory values. Further studies will be needed to inform the robustness of elevated NLR for co-infection detection both in the context of COVID-19 and other viral co-infections such as influenza.
Bacterial co-infection is a major source of morbidity and mortality in the context of respiratory viral infections. A recent retrospective study from Lui et al. reported a 6.8% bacterial co-infection rate with influenza A or B viruses, parainfluenza virus, or respiratory syncytial virus with 10-13% 30-day mortality rate [28]. Our results show that COVID-19 patients with confirmed bacteremic co-infections have double the 30-day mortality rate (UAB: 25%, OLHS: 20%) when compared to influenza virus bacterial co-infections [28]. We determined that COVID-19 bacterial co-infections had a profound impact on increased likelihood of in-hospital mortality, Across both cohorts, the odds ratio for in-hospital mortality for COVID-19 co-infection was higher than the reported mortality odds ratio for influenza virus bacterial co-infection and was independent of SARS-CoV-2 variant [17,28,29]. Importantly, the 26% and 22% in-hospital mortality rates observed in the UAB and OLHS cohorts were fivefold higher than the community-acquired bacteremia encounters from the UAB pre-COVID-19 pandemic comparator cohort (5.9%) These results strongly suggest an underappreciated interaction between bacterial pathogens and SARS-CoV-2, and their impact on clinical outcomes. In addition to the blood culture-positive co-infection group, the suspected co-infection population displayed increased odds ratios for markers of severe disease. This is partially explained by the association of increased disease severity at presentation prompting clinicians to manage the possibility of bacterial co-infection with initiation of antibacterial therapy and collection of blood cultures. However, another consideration is that co-infection for this study was strictly defined to pathogens recovered from blood culture. From a physiologic perspective, coinfection includes a broad variety of organisms involving multiple different tissues. However, accurately differentiating relevant pathogens from recovery of incidental or colonizing organisms is inherently difficult, particularly from sites such as the respiratory tract. Further, recovery of pathogens from the blood is influenced by the presence of antimicrobials prior to culture collection, either as an outpatient or shortly after presentation. Despite the restrictiveness of our approach and the low frequency of bacterial co-infection, our observations attribute a massive effect on morbidity and mortality to co-infection when viewed in context of the estimated 4 million hospitalizations for COVID-19 in the United States [30]. A critical question remains regarding the optimal therapeutic management of high-risk presentations of COVID-19 and potentially other respiratory viral pathogens. Although targeted antimicrobial therapy remains a mainstay of modern management of critically ill patients, results from a 2022 multi-omic study comparing broncho-alveolar lavage samples from influenza virus and COVID-19 co-infections showed that initiation of antimicrobials during COVID-19 co-infection did not alter lung inflammation [31]. Notably, here nearly all patients identified in the co-infected group, and all patients in the suspected co-infection groups, had prompt initiation of antimicrobial treatment. These results suggest that antimicrobials alone may be insufficient to prevent progression to severe disease and worse clinical outcomes in COVID-19 bacterial co-infections. Interestingly, a variety of immune modulators for moderate and severe COVID-19 have been found to improve clinical outcomes, with limited evidence for secondary infections [24,[32][33][34][35]. Collectively, these observations suggest the possibility that targeted immune suppression may be beneficial in managing severe COVID-19 even in the setting of coinfection. Future multicenter studies focused on determining immunological correlates for disease severity and bacterial co-infection are warranted for COVID-19 and other respiratory viral pathogens.